R获取多条简并引物的反向互补序列

primer = read.table(file="primer.txt",sep="\t")

#使用
res = primer.comp(primer,which = 1,rev=TRUE)
write.table(res,file = "primer_comp_rev.txt",sep="\t",col.names = NA,quote = F)

#函数
primer.comp = function(primer,which,rev=TRUE){

  for(i in seq(which,nrow(primer),2) ){ 
    x = toupper(primer[i,2])
    seq = unlist(strsplit(x,NULL))

    new.seq = c()
    for (j in 1:length(seq)){
      if (seq[j]=="A") new.seq[j] = "T"
      if (seq[j]=="G") new.seq[j] = "C"
      if (seq[j]=="C") new.seq[j] = "G"
      if (seq[j]=="T") new.seq[j] = "A"

      if (seq[j]=="Y") new.seq[j] = "R"
      if (seq[j]=="R") new.seq[j] = "Y"
      if (seq[j]=="W") new.seq[j] = "W"
      if (seq[j]=="S") new.seq[j] = "S"
      if (seq[j]=="K") new.seq[j] = "M"
      if (seq[j]=="M") new.seq[j] = "K"

      if (seq[j]=="D") new.seq[j] = "H"
      if (seq[j]=="V") new.seq[j] = "B"
      if (seq[j]=="H") new.seq[j] = "D"
      if (seq[j]=="B") new.seq[j] = "V"
      if (seq[j]=="N") new.seq[j] = "N"
      if (seq[j]=="X") new.seq[j] = "X"
      if (seq[j]=="-") new.seq[j] = "-"
    }

    #是否取反向
    if (rev==TRUE){
      new.seq = rev(new.seq)
      out = c()
      for (r in 1:length(new.seq)){out = paste(out,new.seq[r],sep="")}
      primer[i,2] = out
    } else {
      out = c()
      for (r in 1:length(new.seq)){out = paste(out,new.seq[r],sep="")}
      primer[i,2] = out
      }

  }
 print(primer)
}